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SG-1 finally discovers Dr.Daniel Jackson and is shocked to see that he is a Prior of the Ori. Jackson attempts to convince SG-1 that he was made into a Prior so that he could get Adria to trust him, because he has his own agenda: Jackson plans to wipe out the Ori once and for all by sending the Sangraal to the Alteran Home Galaxy.

SG-1 discovers a planet recently visited by an OriPrior. They learn from Tevaris, the leader of the village, that this Prior, oddly, made no threats whatsoever and spoke only of the merits of Origin. A villager alerts them to the return of the Prior and SG-1 requests that their presence remain hidden. Subsequently, a hooded Prior asks Tevaris if the village is to convert to Origin. Tevaris wants to know more about the Ori and their ways before giving an answer. Without giving any threats, the Prior removes his hood and reveals himself to be Dr.Daniel Jackson. The team immediately returns to Earth to inform Major GeneralHenry Landry.

While reciting Ori teachings to the villagers, Daniel is transported onto the Odyssey. He appears before Teal'c and Lt. ColonelCameron Mitchell, who render him unconscious by a Zat'nik'tel blast (though not before expressing shock at the fact that he said "Hey! What took you guys so long?"). Daniel is physically restrained and the Prior disruptor is used to inhibit his powers. The team is shocked to hear Jackson speaking normally and making no threats on their lives, unlike past incapacitated Priors.

Daniel explains that he let himself be captured as he knew Merlin's consciousness would protect his mind from Adria. During Adria's attempted conversion of Daniel to Origin, Merlin's consciousness protected him, allowing him to remain himself while acquiring the abilities of a Prior. The reason Adria converted Jackson was that she had little choice but to trust him as she felt that he was the best chance of converting Earth (as well as Vala Mal Doran, her biological mother).

Daniel reveals his (and Merlin's) plan to SG-1: By allowing Adria to believe that he had been converted to Origin, Daniel and Merlin were able to work with Adria to complete the Sangraal. Merlin's consciousness surfaces for a moment and tells them that thanks to his protection, Daniel was able to successfully lie to Adria; even with her powers, she was unable to detect it. Adria hoped that the weapon would lead to a swift end to the war with the Ancients. Daniel secretly planned to complete the weapon, pilot an Ori ship through the Supergate, and use the device to eliminate the Ori once and for all. Lt. ColonelSamantha Carter reminds him the Supergate is currently being blocked by the black hole in the PegasusGalaxy. Daniel explains that, in order for the plan to succeed, the gate connection must be broken, albeit with the assistance of SG-1.

Major GeneralJack O'Neill, at Stargate Command, is briefed by the team before boarding the Odyssey. O'Neill and Daniel delve into a heated discussion about their personal lives. Daniel explains that he has very little time before he reverts to his original form; therefore, the plan must be completed soon. Adria will be growing suspicious as to why he has not returned, and Merlin has altered Daniel's DNA so that after a specific passage of time he will revert to his normal state, losing both Merlin’s knowledge and his abilities as a Prior.

O’Neill asks how the Supergate can be deactivated. Daniel says a Mark IX "Gate-Buster" bomb placed behind the gate in the Pegasus galaxy will destroy the Stargate and permanently disconnect the wormhole to the Supergate. Carter confirms a Mark IX placed behind the gate should destroy the Stargate and sever the connection.

Teal'c, visiting Daniel, asks why Adria is not suspicious about him leaving Merlin’s weapon unfinished. Daniel tells him that Adria told him to wait as she feared the Ancients would take action if it was completed. Daniel adds that the Ori need the entire galaxy converted in order to distract the Ancients so that they can use the weapon to destroy the Ancients from a safe distance. Daniel also explains why he was preaching on the planet: he was supposedly doing it to gather more followers on Adria's own orders, but unknown to her, he chose that particular planet because he knew SG-1 was going to go there and he wanted them to capture him.

Teal'c believes Jackson is telling the truth, but the International Oversight Advisory has vetoed the plan even after the team and O'Neill modify it so they can complete it themselves with the intel Daniel gives them. Worse of all, Richard Woolsey hesitantly informs them that Jackson’s life is to be terminated immediately but the team convinces him to freeze Daniel in a stasis pod instead.

Vala informs Daniel about Woolsey's intentions, which Jackson had feared after the Khalek incident. Woolsey visits Daniel to tell him that with Merlin's knowledge in his mind he is to be frozen in stasis, beamed straight into the Ancient pod in Antarctica. Daniel overcomes the Prior disruptor and frees himself. Daniel beams Woolsey back along with the entire crew and beams up O'Neill, as he trusts him to give the command to the Daedalus to destroy the Pegasus gate. They plot a course for the Supergate.

On the way, Daniel reveals that he overpowered the crew and Woolsey before taking control of the ship because he does not believe that SG-1 can complete his plan on their own. Additionally, he did not want to be frozen, something O'Neill agrees with after his own experience with a stasis pod.

SG-1 after beaming onto the Ori ship.

SG-1, minus Daniel and O'Neill, is ringed onto an Ori warship. After encountering some resistance, they find the unfinished Sangraal, as well as the remaining pieces and Daniel's instructions. The Ori ship enters hyperspace and Carter seals off the level, preventing more guards from appearing. Vala starts assembling the weapon piece by piece until only one remains. She says the final piece will initiate the device, leaving five minutes until its activation. Upon its completion, Vala is surprised to see that no ascended Ancient appears and takes the device away from them.

After exiting from hyperspace, SG-1 finds an Ori ship blocking their path to the Supergate. Ori guards appear behind Vala and Mitchell with weapons drawn. Mitchell carefully questions Carter on his radio. He thought she locked off the level. Carter replies with "Me too” as Adria stands before her.

The Odyssey exits hyperspace and immediately cloaks. O’Neill comments that the Ori ships can see them, but Jackson tells him he activated the cloak. O’Neill points out that the ship does not have a cloak and Daniel indicates that it does now, thanks to the Zero Point Module. The duo make preparations to interrupt the Pegasus gate, although O'Neill still remains somewhat suspicious of Daniel.

Daniel beams to the Ori ship and asks Carter and Teal’c how the plan is progressing, but they refuse to answer. Adria cannot sense Daniel's intentions and confronts him. Daniel fires an energy blast from his hand using his abilities as a Prior which knocks her unconscious. Daniel reveals he held the Prior disruptor behind his back to prevent Adria from reading his mind or fighting back, and that he was able to focus his powers sufficiently to defeat her personal shield. He tells Carter that O’Neill is on the Odyssey and can give the command and beam them back. Daniel, now weak, moves to the Ori Control chair and tells Carter and Teal’c to arm the Ancient device. They take out the guards, and with Vala and Mitchell arm the device. Daniel moves the other Ori ship away from the Supergate and tells O’Neill to contact the Daedalus to destroy the Pegasus gate. After a moment of hesitation, O'Neill gives the order. The Supergate shuts down. Daniel re-opens the Supergate and directs the Ori ship towards the wormhole. SG-1 returns to the bridge to find Daniel unconscious and no longer a Prior. Carter tells O’Neill to beam them onto the Odyssey. Vala worries about Adria as O'Neill beams them out and they leave her behind. The Ori ship enters the wormhole and the Supergate shuts down.

Seven Ori ships leave the Supergate

Daniel wakes in the infirmary of the Odyssey and convinces O'Neill he no longer has Merlin's consciousness within him. The team wonders whether the device worked. Carter informs everyone that the Supergate has started dialing, and it soon activates. From the bridge the team watches as six Ori ships come through the gate and jump with the seventh into hyperspace.

O'Neill: Carter doesn't think it can be done.Jackson: Yes it can. A Mark IX beamed directly behind the gate in the Pegasus galaxy will destroy that gate, the wormhole connection will be broken.O'Neill: How do you know that?Jackson: Hello!! Merlin!!O'Neill: Oh yes, (mockingly) Merlin!!Jackson: Jack, I wish I had proof. I wish I had a way to convince you, but I don't. Now, this is the only choice I had, and I took it. It's a good﻿ plan, it-it-it just happens to hinge on you guys believing in me, having a little faith... now, I thought you of all people might!!O'Neill: WHY!?!? You of all people should know that I don't believe anything anybody says, even if I understand what they're talking about!! (confusedly looks away)

Woolsey: I ... you have to understand: we've considered all the evidence at our disposal, but more than that, as difficult as this is, I feel very strongly that we have no viable option.Mitchell: (standing up) You want to get to the point?Woolsey: I assure you, this may be the hardest decision I'll ever make, but I take full responsibility for it. Based on my recommendation, the IOA has proposed to the President that Daniel Jackson's life be terminated immediately.

Jackson: (to Vala) I thought Teal'c believed me.Vala: Oh, he does.Jackson: Jack?Vala: No, he's on your side, too.(Jackson gives Vala a questioning look.)Vala: That little weasel man who somehow represents your government.Jackson: Woolsey?Vala: I can't be certain, but I think he might not like you.Jackson: He wants to have me killed, doesn't he?Vala: I'm not sure how serious he is. He seems quite the prankster to me.Jackson: You know, I was afraid of that. He was the one who argued to keep Khalek alive and got burned for it.

Vala: But not to worry. If it comes down to it, I have a plan.Jackson: Oh, you have a plan. Great. What is it?Vala: Well, when I said that I had a plan, I meant that I have to plan the plan. So when, or rather, if it comes down to it, I will have a plan. I've cleared my whole afternoon, for planning.Jackson: (incredulous) You believe me, right?Vala: Mmm-hmm.Jackson: Okay, now I don't believe you.Vala: (picks up a stool and sits down) Imagine our positions were reversed. What would you do?Jackson: Hmm...Vala: I know you've trusted me even when you've had every reason not to, but perhaps I'm the only one who knows how dangerous and powerful Adria is. There's no evidence. Only your word, and that should be enough, but this is so big.Jackson: Well, I wouldn't let them kill you.Vala: Of course not. I won't let that happen to you. But would you support me, if what I was proposing could very well open the door to the final Ori victory?

O'Neill: Yep. Just like old times. Except... I'm here against my will, and you look like Marcel Marceau.Jackson: Yeah, ya know, some things change, but others stay the same.

O'Neill: Then why do this now?Jackson: Because I'm afraid the rest of the team won't be able to complete the mission without me.O'Neill: Oh, aren't we full of ourselves.Jackson: That, and I wasn't about to let Woolsey freeze me.O'Neill: That, I understand.Jackson: Yeah.

Carter: (over the radio) Vala, Cam, we're moments away from exiting hyperspace.Mitchell: (into the radio) Roger that. We're almost done here. Check that, uh, Vala's almost done, I still have my doubts.Vala: (places the Sangraal crystal into the top of the weapon, it begins to glow)Mitchell: And that means...?Vala: That means the weapon is ready to be activated. (suddenly starts fearfully looking around in circles)Mitchell: What?Vala: Oh, I was just wondering if an ascended being was going to swoop down and take it away.Mitchell: I guess they don't mind us doing their dirty work for 'em.Vala: Or...Mitchell: Or what?Vala: Or there's no point because I've assembled it wrongly and it's not going to work.

There are now eight Ori warships in the Milky Way. Four arrived in "Camelot" and six in this episode. One ship was lost when the Supergate was activated in "The Pegasus Project" and one left through the Supergate in this episode (although it is possible that it came back as one of the incoming six - because Adria was on board, and she obviously returned to this galaxy). The entire crew of another ship was killed in "Counterstrike" by the Ancient superweapon on Dakara, but the ship remained intact and was apparently re-crewed with personnel from the other ships.

It is confirmed that a Mark IX "Gatebuster" can destroy an active Stargate. The previous time the device was used (i.e., in "Beachhead") the Gate remained intact due to a local Prior extending a shield around it.

In the alternate reality visited by Sam in "The Road Not Taken", the Daniel Jackson of that reality was likewise captured by the Ori during an alternate version of the events of "The Quest, Part 2", though it is unknown if he was also converted into a Prior or had Merlin's consciousness transferred into his mind as occurred to the Daniel of our reality prior to the events of this episode.

After Daniel beamed O'Neill to the Daedalus, O'Neill makes a comment about how Daniel looks like Marcel Marceau who was a French actor and mime most famous for his stage persona as "Bip the Clown." While Daniel (and most priors for that matter) did, in fact, look like a mime in classic face paint this reference is also, likely, a nod to Richard Dean Andersons' time working as a street mime.

When Major GeneralJack O'Neill and Dr.Daniel Jackson have their first meeting in this episode, Jack's uniform has only the single star of a Brigadier General on his collar, rather than the two stars of a Major General he should have. Later, when SG-1 have their two meetings in the briefing room with O'Neill, he is wearing two stars. O'Neill also refers to Major GeneralHenry Landry as "sir" despite them being the same rank and O'Neill holding an office above Landry. However, given O'Neill's penchant for being sarcastic, this could simply be a joke.

When O'Neill and Daniel are talking the first time O'Neill goes to the back of the room to get a chair there is a TV with a video feed from a security camera in the room and in the feed you can see O'Neill sitting down in the chair before he really does.

When the Odyssey is in hyperspace, the shot is mirrored with the "tower" on the ship being on the right side, not the left.

Daniel's aged prior look make-up, specifically the talc in his hair, rubs off on the chair he is restrained in.

As the Ori ships emerge from the Supergate at the end of the episode, the second Ori ship's trail disappears as the ship goes offscreen.